User: meerapprasad

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meerapprasad10
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11 months, 2 weeks ago
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1 year, 6 months ago
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Posts by meerapprasad

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Comment: C: Samtools view error when converting sam to bam file using sc-ATAC-seq data from
... 1300:@RG ID:A2.08,P2.14,A1.04,P1.05 SM:Barcode05838 4099:@PG ID:bowtie2-E6859AC-EAA2107 PN:bowtie2 VN:2.2.5 CL:"/mnt/users/sai/miniconda2/bin/bowtie2-align-s --wrapper basic-0 -X2000 -p 18 --rg-id kidney_marrow_KO_gata2B -x /mnt/users/sai/Script/genomes/bowtie2/GRCz10/GRCz10 -1 /mnt/AlignedData/181 ...
written 11 months ago by meerapprasad10
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Comment: C: Samtools view error when converting sam to bam file using sc-ATAC-seq data from
... Hi! Thank you so much for the reply! I tried what you had suggested but got the same error: [W::sam_read1] Parse error at line 1 [main_samview] truncated file. Do you have any other recommendations? ...
written 11 months ago by meerapprasad10
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Comment: C: Samtools view error when converting sam to bam file using sc-ATAC-seq data from
... Hi John, Thank you so much for the reply! I am new to samtools so I am not sure what the numbers before the @RG are, but I tried what you had suggested and got this error: [E::sam_parse1] missing SAM header [W::sam_read1] Parse error at line 191 [main_samview] truncated file. What do you recomm ...
written 11 months ago by meerapprasad10
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Samtools view error when converting sam to bam file using sc-ATAC-seq data from Cell Ranger pipeline
... Hi! I am working on a single cell ATAC sequencing project and am having an issue using samtools to split a bam file based on my wild-type and knock-out. The data came from 10X sequencing and they used the Cell Ranger pipeline for analysis. One analysis that the Cell Ranger conducted was t-sne which ...
samtools view samtools cell ranger sc-atac-seq written 11 months ago by meerapprasad10 • updated 11 months ago by John Marshall2.0k
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Comment: C: "bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out h
... Hi Gautier, Thank you! I have been in contact with our HPC - expert and he has helped me up the RAM as much as possible. Unfortunately, it still has not been working. Would you recommend another alignment such as BWA? ...
written 18 months ago by meerapprasad10
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Comment: C: "bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out h
... Hello! Yes, I think we have been running out of memory. Are you familiar with any other ways to map our sequences to this database? ...
written 18 months ago by meerapprasad10
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"bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out how to fix my script
... Hello! I am working on assembling a transcriptome of the terminal ganglion of the cricket (Gryllus bimaculatus). We are working on a non-model species and thus did not remove ribosomal contamination during library prep. We want to remove ribosomal contamination bioinformatically, and I am mapping ou ...
software error assembly alignment bowtie2 written 18 months ago by meerapprasad10 • updated 16 months ago by Biostar ♦♦ 20

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